Transcription in higher eukaryotes, like humans, is a complex process in which transcription factors can regulate gene expression by binding far upstream, downstream, or within the introns of genes. Computational methods have been developed to predict such interactions, however only a small subset of predicted transcription binding sites are used in vivo. The main goal of this proposal is to develop protocols and techniques that will facilitate the detection of in vivo transcription factors binding sites (TFBSs) in humans and other mammalian genomes. Knowing the basis behind TFBS binding will further our understanding of development, tissue-specific expression, and disease. To address these issues the following specific aims are proposed for this study: 1) To develop a high-resolution chromatin immunoprecipitation microarray (ChlP-chip) protocol to identify in vivo binding sites of skeletal muscle differentiation-specific transcription factors in human and mouse myoblast cells; 2) To perform a genome-wide comparison of in vivo transcription factor binding sites in mouse and human skeletal muscle to discover clustering patterns of transcription factors within the regulatory regions of skeletal muscle-specific genes.